Failed to run function getTable under certain condtion

[chengmingbo]

Hi there,

Under certain condition, getTable function will throw an error.
The problem emerges when machine[[i]] == character(0).
I just fixed the problem by changing the code here:

  tab = do.call(rbind, lapply(1:ncol(fc), function(i) {
    lastcol = colnames(gs$specScore)[i]
    if(length(machine[[i]]) <= 0){
      lastcol = character(0)
    }
    data.frame(fc[which(rownames(fc) %in% 
    machine[[i]]), i], pp$adjpval[which(rownames(pp$adjpval) %in% 
    machine[[i]]), i], gs$specScore[which(rownames(gs$specScore) %in% 
    machine[[i]]), i], lastcol)}))

[mahmoudibrahim]

Hi

awesome..thanks for finding and fixing this bug :)

let me know if you would like to make a pull request. Otherwise, I will incorporate the changes and release a new version in the next few days!

best wishes
Mahmoud

[mahmoudibrahim]

Hi @chengmingbo

I've actually noticed another additional bug with getTable. So I rewrote the function, fixed the bugs and also made it much faster.

The new release includes all the edits:
https://github.com/mahmoudibrahim/genesorteR/releases/tag/v0.4.0

best wishes
Mahmoud

[mahmoudibrahim]

hi again @chengmingbo

there was still a bug in there, not enough caffeine this morning :) - should be bug-free now as far as I can tell, but please let me know if it still breaks

https://github.com/mahmoudibrahim/genesorteR/releases/tag/v0.4.1

best wishes
Mahmoud

[chengmingbo]

hi again @chengmingbo

there was still a bug in there, not enough caffeine this morning :) - should be bug-free now as far as I can tell, but please let me know if it still breaks

https://github.com/mahmoudibrahim/genesorteR/releases/tag/v0.4.1

best wishes
Mahmoud

Hi, Mahmoud,
Thanks for your information, it is good to know, I will try it later on.

[sidwekhande]

Hi Mahmoud,

This bug may not be from your side, but it is related to the getTable() function and this is just so you are aware of it:

When I run getTable(sg, pv), I get the following error -

getTable(sg, pv)
Error in isFALSE(fc_cutoff) : could not find function "isFALSE"

I did some digging, and it goes back to the R version (I am running 3.4.3). This issue (r-spatial/mapview#177) references it as well.
Using !is.null(x) && !isTRUE(x) is something you could consider so that you do not have to have the R version > 3.5 requirement :)

genesorteR is a great package, loved it!

[mahmoudibrahim]

Hi Siddarth

Thank you so much for looking into this, and for the suggestion! I wasn't aware of that R version issue.

I will implement the change and release a new version in the next couple of days. Will update this issue then.

best wishes
Mahmoud

[mahmoudibrahim]

Hi @sidwekhande

I've now released a new version without the dependency on isFALSE:

https://github.com/mahmoudibrahim/genesorteR/releases/tag/v0.4.2

if you are using an older version, please consider installing the newest version.

best wishes
Mahmoud